Briefings in Bioinformatics Advance Access published online on August 9, 2006
Briefings in Bioinformatics, doi:10.1093/bib/bbl027
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* To whom correspondence should be addressed. In recent years, as a knowledge-based discipline, bioinformatics has been made more computationally amenable. After its beginnings as a technology advocated by computer scientists to overcome problems of heterogeneity, ontology has been taken up by biologists themselves as a means to consistently annotate features from genotype to phenotype. In medical informatics, artifacts called ontologies have been used for a longer period of time to produce controlled lexicons for coding schemes. In this article, we review the current position in ontologies and how they have become institutionalized within biomedicine. As the field has matured, the much older philosophical aspects of ontology have come into play. With this and the institutionalization of ontology has come greater formality. We review this trend and what benefits it might bring to ontologies and their use within biomedicine. Olivier Bodenreider is a Staff Scientist in the Cognitive Science Branch of the Lister Hill National Center for Biomedical Communications at the U.S. National Library of Medicine. His research interests include terminology, knowledge representation and ontology in the biomedical domain, both from a theoretical perspective and in their application to natural language understanding, reasoning, information visualization and interoperability. Robert Stevens is a Senior Lecturer in bioinformatics in the School of Computer Science, University of Manchester, U.K. He has degrees in biochemistry, biological computation and computer science. He was a member of the ground breaking TAMBIS project, which was the first in bioinformatics to use description logic ontology to form a homogenizing query layer over bioinformatics resources. Interest in the use of formal ontology has continued in the development of semantic similarity metrics over ontologically annotated corpora. His other work includes the development of methodologies to migrate ontologies from the informal to formal and use reasoning to increase structural validity. His current work includes the use of protein family ontologies to catalog proteins in genomes and the use of ontologies to describe in silico experiments. He has co-chaired the annual bio-ontologies meeting at ISMB for many years and is a co-developer of a highly successful OWL training course.
Received June 23, 2006
Accepted July 10, 2006
Original Papers
Bio-ontologies: current trends and future directions
Olivier Bodenreider * and Robert Stevens
Olivier Bodenreider, E-mail: olivier{at}nlm.nih.gov
Abstract
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